3.GTA particles come in two sizes.Small particles contain 4 kb DNA fragments.The hypothetical large particles contain
fragments that must be at least 14 kb (the size of the GTA gene cluster) but
could be as big as 50 kb.

4.The number of GTA particles a cell produces does
not depend on the proportion of small and large particles.

5.DNA packaging by GTA is random; all parts of the
cell’s genome are equally represented.But in this model we only consider the particles containing the
full-length GTA cluster.

6.This is the killer: If the cell’s
chromosome is 5 MB and the large-particle capacity is 15 kb, only 2x10-4
of large particles will contain complete GTA gene clusters (will be G+
particles).If we change the
large-particle capacity to 20 kb, then about 1x10-3 of large
particles will contain a complete cluster.A 50 kb capacity and a 3 MB chromosome would probably get it up to about
10-2.(And this
ignores the recombination machinery’s need for homologous DNA flanking the GTA
cluster to promote recombination.)

Transduction:

7.GTA- cells completely lack the main GTA gene
cluster.They can only be converted to
GTA+ by homologous recombination with GTA-containing DNA from G+ particles.

8.GTA particles cannot tell the difference between
GTA+ and GTA- recipients.Particles
capable of transducing GTA- cells to GTA+ can also ‘transduce’ GTA+ cells to
GTA+.

9.All GTA particles produced in one cycle are
taken up by and transduce cells in that cycle.(The efficiency of infection and recombination is 1.)

10.The
model ignores large and small GTA particles that don’t transduce GTA+.

11.Each
cell takes up only one G+ particle (or none).This is reasonable, since the number of G+ particles is always going to
be much smaller than the number of cells.

bNumber of GTA particles produced by each burst.Default value is 100.(We have no actual measurements.)

µFraction of GTA particles that are large.(We expect this fraction to be small, since
large particles have not been observed.)

TFraction of large GTA particles that are G+ particles (able to
transduce GTA).(This is limited by
genome size, GTA gene cluster size, and the DNA capacity of these hypothetical
particles.Plausible values are between
10-2 and 10-4.)

Gµ
* T Fraction of GTA particles that contain complete GTA genes.

What happens in one generation:

GTA production and cell lysis:

NProportion of GTA particles to cells remaining in the medium after
GTA+ cells have burst.

=
(Fcb)/(1 – Fc)(Note: Fcb
is the GTA production per original cell. 1 – Fc
normalizes this to the number of cells remaining after lysis.)

N+Proportion of GTA particles, per remaining cell,
that carry the complete GTA gene cluster (are ‘G+’ particles able to transduce
the GTA-production genotype to GTA- cells).

If the culture were more dilute or
poorly mixed, some GTA particles would not find new cells to attach to.This would reduce the amount of transduction
(effectively reducing W).

GTA
production:

3.GTA particles come in two sizes.Small particles contain 4 kb DNA fragments.The hypothetical large particles contain
fragments that must be at least 14 kb (the size of the GTA gene cluster) but
could be as big as 50 kb.

This is the central assumption of the
model.The size of the small particles
is known.The hypothesized large
particles could be as small as 15 kb (allows a bit of homologous sequence on
each side of the cluster to promote recombination).Phage capsids can in principle be very large,
but it’s parsimonious to assume a modest size.

4.The number of GTA particles a cell produces
does not depend on the proportion of small and large particles.

Large capsids will require more
capsid protein molecules.

5.DNA packaging by GTA is random; all parts of
the cell’s genome are equally represented.But in this model we only consider the particles containing the
full-length GTA cluster.

Experimental results show slightly less
packaging of GTA sequences.If this
applies to the hypothetical large particles it would reduce production of G+
particles.If particles preferentially
package GTA, GTA would be a phage.

6.This is the killer: If the cell’s chromosome is 5 MB and the
large-particle capacity is 15 kb, only 2x10-4 of large particles
will contain complete GTA gene clusters (will be G+ particles).If we change the large-particle capacity to
20 kb, then about 1x10-3 of large particles will contain a complete
cluster.A 50 kb capacity and a 3 MB
chromosome would probably get it up to about 10-2.(And this ignores the recombination
machinery’s need for homologous DNA flanking the GTA cluster to promote
recombination.)

See point 3 above.

Transduction:

7.GTA- cells completely lack the main GTA gene
cluster.They can only be converted to
GTA+ by G+ particles.

Transduction depends on homologous
recombination.Small GTA particles can
transduce functional alleles of individual GTA genes, replacing versions that
became mutated or even deleted in an ancestor of the recipient cell.But they cannot introduce GTA genes into
cells that completely lack the GTA cluster, because there will be no homologous
sequences to recombine with.

8.GTA particles cannot tell the difference
between GTA+ and GTA- recipients.Particles capable of transducing GTA- cells to GTA+ can also ‘transduce’
GTA+ cells to GTA+.

I think some phages and conjugative
plasmids may be able to detect whether potential hosts/recipients already have
the element, but we have no evidence that transduction frequencies differ
between GTA+ and GTA- recipients.Wall
et al (1975) surveyed 33 strains and found wide variation in both GA production
and transduction, but no correlation between these abilities.

9.All GTA particles produced in one cycle are
taken up by and transduce cells in that cycle.(The efficiency of infection and recombination is 1.)

This is unlikely to be true, but assuming
this increases the chance that each G+ particle successfully transduces a GTA-
cell to GTA+.

If we were to relax this assumption the
model would need to include an explicit uptake process and to specify what
happens to particles that are not taken up.

10. The model ignores large and small
GTA particles that don’t transduce GTA+.

This should be OK, since these should
not interfere with transduction by G+ particles, especially because their total
number per cell will be small. Removing this assumption would make GTA + spread
less likely.

11. Each cell takes up only one G+
particle (or none).

This is a reasonable assumption, since
the number of G+ particles is always going to be much smaller than the number
of cells.If the number of G+ particles
were high, sometimes two G+ particles might inject their DNAs into the same
s=cell, which would reduce the efficiency of transduction.